[gmx-users] differ version of gromacs

Dear Users, Is in Gromacs any possibilty to convert data from higher version (5.1.2) (command trjconv) by using lower version of Gromacs? Thank you in advance, Marta -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before

[gmx-users] error - decomposition

Dear Users, I have problem with ranks: Fatal error: There is no domain decomposition for 288 ranks that is compatible with the given box and a minimum cell size of 1.02425 nm Change the number of ranks or mdrun option -rcon or -dds or your LINCS settings I change the size of box, but it doesn't h

[gmx-users] time in restarting job

Dear Users, I am a bit confused. I'd like extend my simulation. For it I used command: grompp -f prod.mdp -c prod.tpr -o prod_ext.tpr -t prod.cpt mdrun -s prod_ext.tpr But now I have 2 simulation (first md) 0-100ns and extended 0-50ns. How to extend time? Because after trjcat .trr files I'd like

Re: [gmx-users] Did not find any molecules of type ...

t your Subject line so it is more specific > than "Re: Contents of gromacs.org_gmx-users digest..." > > > Today's Topics: > >1. Temperature Calculation in MD (Ray Chao) > 2. Re: Temperature Calculation in MD (Justin Lemkul) >3. Did not find any

[gmx-users] Did not find any molecules of type ...

Dear all, I'd like perform a free energy binding calculations. I defined my molecules by WAT moleculetype in topology and these same name in gro file. I didn't include a wat.itp file to .top file. During grompp command, it shown up an error: Fatal error: Did not find any molecules of type 'WAT'

[gmx-users] free energy calculations

Dear Gromac's users, I'd like to perform a FEP calculations. I've done yours tutorial and now follow by it, i'd like to perform my calculations for small molecule in water. I got a problem: Fatal error: No such moleculetype SOL I don't know what it means in these cases, because both files are sim

[gmx-users] trivial question about water molecules

Hello Gromacs Users; I'd like to calculate the # of replaced water molecules by sodium chloride in my system . I added a 0.15M concentration of NaCl. How can I calculate the number of water molecules, which are replaced by ions? Thank you in advance, Marta -- Gromacs Users mailing list * Please

[gmx-users] doubled atoms

Hello, In my file, I found artifact. One side-chain of amino-acid has got a doubled the last one atom. I got two O2 atoms instead one O (from carboxylic moiety). What should I do? If I will delete it, I'll get the incorrect numbering. Thank you in advance. Bests, Marta -- Gromacs Users mailing

[gmx-users] preapration of non-standard residue

Dear Gromacs Users, I'd like to prepare my system for MD simulations. I have non-standard residue. I prepared a topology and coordinates by antechamber. I know, I should add it to itp file. But what exactly I should do? Thank you in advance, Marta -- Gromacs Users mailing list * Please search

[gmx-users] atom numbering

Dear Gromacs users, My problem focus on number order. I am preparing my system to md. In my pdb file I made a some modifications (delete chains or ligand compounds). During preparation of topology and gro file, the residue number ordering is changed. Is there any possibility to preserve number ord

[gmx-users] atom numbering

Dear Gromacs users, My problem focus on number order. I am preparing my system to md. In my pdb file I made a some modifications (delete chains or ligand compounds). During preparation of topology and gro file, the residue number ordering is changed. Is there any possibility to preserve number ord